tetano
Editor, Senior Moderator
J Med Virol
. 2020 Dec 21.
doi: 10.1002/jmv.26744. Online ahead of print.
A comparative insight into genomic landscape of SARS-CoV-2 and identification of mutations associated with origin of infection and diversity
Divya Mishra[SUP] 1 [/SUP], Gurparsad Singh Suri[SUP] 2 [/SUP], Gurleen Kaur[SUP] 2 [/SUP], Manish Tiwari[SUP] 3 [/SUP]
Affiliations
Abstract
The analyses of 2325 SARS-CoV-2 genomes revealed 107, 162 and 65 nucleotide substitutions in the coding region of SARS-CoV-2 from the three continents America, Europe and Asia, respectively. Of these nucleotide substitutions 58, 94 and 37 were nonsynonymous types mostly present in the Nsp2, Nsp3, Spike and ORF9. A continent-specific phylogram analyses clustered the SARS-CoV-2 in the different group based on the frequency of nucleotide substitutions. Detailed analyses about the continent-specific amino acid changes and their effectiveness by SNAP2 software was investigated. We found 11 common nonsynonymous mutations, out of them two novel effective mutations were identified in ORF9 (S194L and S202N). Intriguingly, ORF9 encodes nucleocapsid phosphoprotein possessing many effective mutations across continents and could be a potential candidate after the spike protein for studying the role of mutation in viral assembly and pathogenesis. Among the two form of certain frequent mutation one form is more prevalent in Europe continents (Nsp12:L314, Nsp13
504, Nsp13:Y541, Spike:G614 and ORF8:L84) while other forms is more prevalent in American (Nsp12314, Nsp13:L504, Nsp13:C541, Spike
614 and ORF8:L84) and Asian continents (Spike614) indicating the spatial and temporal dynamics of SARS-CoV-2. We identified highly conserved 38 regions and among these regions, 11 siRNAs were predicted on stringent criteria that can be used to suppress expression of viral genes and corresponding reduction of human viral infections. Present investigation provides information of different mutations and will pave the way for differentiating strains based on virulence and their use in development of a better antiviral therapy. This article is protected by copyright. All rights reserved.
Keywords: Coronavirus; Mutation; Phylogeny; Synonymous and nonsynonymous substitutions; siRNA.
. 2020 Dec 21.
doi: 10.1002/jmv.26744. Online ahead of print.
A comparative insight into genomic landscape of SARS-CoV-2 and identification of mutations associated with origin of infection and diversity
Divya Mishra[SUP] 1 [/SUP], Gurparsad Singh Suri[SUP] 2 [/SUP], Gurleen Kaur[SUP] 2 [/SUP], Manish Tiwari[SUP] 3 [/SUP]
Affiliations
- PMID: 33347622
- DOI: 10.1002/jmv.26744
Abstract
The analyses of 2325 SARS-CoV-2 genomes revealed 107, 162 and 65 nucleotide substitutions in the coding region of SARS-CoV-2 from the three continents America, Europe and Asia, respectively. Of these nucleotide substitutions 58, 94 and 37 were nonsynonymous types mostly present in the Nsp2, Nsp3, Spike and ORF9. A continent-specific phylogram analyses clustered the SARS-CoV-2 in the different group based on the frequency of nucleotide substitutions. Detailed analyses about the continent-specific amino acid changes and their effectiveness by SNAP2 software was investigated. We found 11 common nonsynonymous mutations, out of them two novel effective mutations were identified in ORF9 (S194L and S202N). Intriguingly, ORF9 encodes nucleocapsid phosphoprotein possessing many effective mutations across continents and could be a potential candidate after the spike protein for studying the role of mutation in viral assembly and pathogenesis. Among the two form of certain frequent mutation one form is more prevalent in Europe continents (Nsp12:L314, Nsp13
504, Nsp13:Y541, Spike:G614 and ORF8:L84) while other forms is more prevalent in American (Nsp12314, Nsp13:L504, Nsp13:C541, Spike614 and ORF8:L84) and Asian continents (Spike614) indicating the spatial and temporal dynamics of SARS-CoV-2. We identified highly conserved 38 regions and among these regions, 11 siRNAs were predicted on stringent criteria that can be used to suppress expression of viral genes and corresponding reduction of human viral infections. Present investigation provides information of different mutations and will pave the way for differentiating strains based on virulence and their use in development of a better antiviral therapy. This article is protected by copyright. All rights reserved.Keywords: Coronavirus; Mutation; Phylogeny; Synonymous and nonsynonymous substitutions; siRNA.